|
1
|
Ma Q, Liu HS, Li HJ, Bai WP, Gao QF, Wu SD, Yin XX, Chen QQ, Shi YQ, Gao TG, Bao AK, Yin HJ, Li L, Rowland O, Hepworth SR, Luan S, Wang SM. Genomic analysis reveals phylogeny of Zygophyllales and mechanism for water retention of a succulent xerophyte. PLANT PHYSIOLOGY 2024; 195:617-639. [PMID: 38285060 DOI: 10.1093/plphys/kiae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/30/2023] [Accepted: 12/21/2023] [Indexed: 01/30/2024]
Abstract
Revealing the genetic basis for stress-resistant traits in extremophile plants will yield important information for crop improvement. Zygophyllum xanthoxylum, an extant species of the ancient Mediterranean, is a succulent xerophyte that can maintain a favorable water status under desert habitats; however, the genetic basis of this adaptive trait is poorly understood. Furthermore, the phylogenetic position of Zygophyllales, to which Z. xanthoxylum belongs, remains controversial. In this study, we sequenced and assembled the chromosome-level genome of Z. xanthoxylum. Phylogenetic analysis showed that Zygophyllales and Myrtales form a separated taxon as a sister to the clade comprising fabids and malvids, clarifying the phylogenetic position of Zygophyllales at whole-genome scale. Analysis of genomic and transcriptomic data revealed multiple critical mechanisms underlying the efficient osmotic adjustment using Na+ and K+ as "cheap" osmolytes that Z. xanthoxylum has evolved through the expansion and synchronized expression of genes encoding key transporters/channels and their regulators involved in Na+/K+ uptake, transport, and compartmentation. It is worth noting that ZxCNGC1;1 (cyclic nucleotide-gated channels) and ZxCNGC1;2 constituted a previously undiscovered energy-saving pathway for Na+ uptake. Meanwhile, the core genes involved in biosynthesis of cuticular wax also featured an expansion and upregulated expression, contributing to the water retention capacity of Z. xanthoxylum under desert environments. Overall, these findings boost the understanding of evolutionary relationships of eudicots, illustrate the unique water retention mechanism in the succulent xerophyte that is distinct from glycophyte, and thus provide valuable genetic resources for the improvement of stress tolerance in crops and insights into the remediation of sodic lands.
Collapse
Affiliation(s)
- Qing Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Hai-Shuang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Hu-Jun Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Wan-Peng Bai
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Qi-Fei Gao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Sheng-Dan Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Xiu-Xia Yin
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Qin-Qin Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Ya-Qi Shi
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Tian-Ge Gao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Ai-Ke Bao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Hong-Ju Yin
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Li Li
- Institute of Grassland, Xinjiang Academy of Animal Science, Urumqi 830000, China
| | - Owen Rowland
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Shelley R Hepworth
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Suo-Min Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| |
Collapse
|
|
2
|
Kalfusová R, Herklotz V, Kumke K, Houben A, Kovařík A, Ritz CM, Lunerová J. Epigenetic histone H3 phosphorylation marks discriminate between univalent- and bivalent-forming chromosomes during canina asymmetrical meiosis. ANNALS OF BOTANY 2024; 133:435-446. [PMID: 38127060 PMCID: PMC11006542 DOI: 10.1093/aob/mcad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND AND AIMS Dogroses (Rosa sect. Caninae) are mostly pentaploid, bearing 2n = 5x = 35 chromosomes in somatic cells. They evolved a unique form of asymmetrical meiosis characterized by two types of chromosomes: (1) chromosomes forming bivalents and distributed in the normal sexual way; and (2) chromosomes occurring as univalents and transferred by a female gamete only. In the mature pollen of pentaploid species, seven bivalent-derived chromosomes are transmitted to offspring, and 21 unpaired univalent chromosomes are eliminated during microsporogenesis. To discriminate between bivalent- and univalent-forming chromosomes, we studied histone H3 phosphorylation patterns regulating meiotic chromosome condensation and segregation. METHODS We analysed histone modification patterns during male canina meiosis in two representative dogrose species, 5x Rosa canina and 5x Rosa rubiginosa, by immunohistochemical and molecular cytogenetics approaches. Immunostaining of meiotic cells included α-tubulin, histone H3 phosphorylation (H3S10p, H3S28p and H3T3p) and methylation (H3K4me3 and H3K27me3) marks. In addition, fluorescent in situ hybridization was carried out with an 18S rDNA probe. KEY RESULTS In the first meiotic division, univalent chromosomes underwent equational division into chromatids, while homologues in bivalents were segregated as regular dyads. In diakinesis, bivalent chromosomes displayed strong H3 phosphorylation signals in proximal regions, spreading to the rest of the chromosome. In contrast, in univalents, the H3 phosphorylation signals were weaker, occurring mostly outside proximal regions largely overlapping with the H3K4me3 signals. Reduced phosphorylation was associated with relative under-condensation of the univalent chromosomes, particularly at early diakinesis. CONCLUSIONS We hypothesize that the absence of pairing and/or recombination in univalent chromosomes negatively affects the histone H3 phosphorylation of their chromatin and perhaps the loading of meiotic-specific cohesins. This apparently destabilizes cohesion of sister chromatids, leading to their premature split in the first meiotic division.
Collapse
Affiliation(s)
- Radka Kalfusová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Veit Herklotz
- Senckenberg Museum of Natural History, Senckenberg – Member of the Leibniz Association, Am Museum 1, 02826 Görlitz, Germany
| | - Katrin Kumke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Christiane M Ritz
- Senckenberg Museum of Natural History, Senckenberg – Member of the Leibniz Association, Am Museum 1, 02826 Görlitz, Germany
- Chair of Biodiversity of Higher Plants, Technical University Dresden, D-01069, Dresden, Germany
| | - Jana Lunerová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| |
Collapse
|
|
3
|
Wang Y, Li X, Feng Y, Wang J, Zhang J, Liu Z, Wang H, Chen T, He W, Wu Z, Lin Y, Zhang Y, Li M, Chen Q, Zhang Y, Luo Y, Tang H, Wang X. Autotetraploid Origin of Chinese Cherry Revealed by Chromosomal Karyotype and In Situ Hybridization of Seedling Progenies. PLANTS (BASEL, SWITZERLAND) 2023; 12:3116. [PMID: 37687365 PMCID: PMC10490022 DOI: 10.3390/plants12173116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/10/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
Polyploidy is considered a driving force in plant evolution and diversification. Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don], an economically important fruit crop native to China, has evolved at the tetraploid level, with a few pentaploid and hexaploid populations. However, its auto- or allo-polyploid origin remains unclear. To address this issue, we analyzed the ploidy levels and rDNA chromosomal distribution in self- and open-pollinated seedling progenies of tetraploid and hexaploid Chinese cherry. Genomic in situ hybridization (GISH) analysis was conducted to reveal the genomic relationships between Chinese cherry and diploid relatives from the genus Cerasus. Both self- and open-pollinated progenies of tetraploid Chinese cherry exhibited tetraploids, pentaploids, and hexaploids, with tetraploids being the most predominant. In the seedling progenies of hexaploid Chinese cherry, the majority of hexaploids and a few pentaploids were observed. A small number of aneuploids were also observed in the seedling progenies. Chromosome 1, characterized by distinct length characteristics, could be considered the representative chromosome of Chinese cherry. The basic Chinese cherry genome carried two 5S rDNA signals with similar intensity, and polyploids had the expected multiples of this copy number. The 5S rDNA sites were located at the per-centromeric regions of the short arm on chromosomes 4 and 5. Three 45S rDNA sites were detected on chr. 3, 4 and 7 in the haploid complement of Chinese cherry. Tetraploids exhibited 12 signals, while pentaploids and hexaploids showed fewer numbers than expected multiples. Based on the GISH signals, Chinese cherry demonstrated relatively close relationships with C. campanulata and C. conradinae, while being distantly related to another fruiting cherry, C. avium. In combination with the above results, our findings suggested that Chinese cherry likely originated from autotetraploidy.
Collapse
Affiliation(s)
- Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu 611130, China
| | - Xueou Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Yan Feng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Rural Revitalization Service Center, Agricultural and Rural Bureau of Cuiping District Yibin City, Yibin 644000, China
| | - Juan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Jing Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Zhenshan Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Hao Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Tao Chen
- College of Life Sciences, Sichuan Agricultural University, Ya’an 625014, China;
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu 611130, China
| | - Zhiwei Wu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu 611130, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu 611130, China
| |
Collapse
|
|
4
|
Lunerová J, Vozárová R. Preparation of Male Meiotic Chromosomes for Fluorescence In Situ Hybridization and Immunodetection with Major Focus on Dogroses. Methods Mol Biol 2023; 2672:337-349. [PMID: 37335487 DOI: 10.1007/978-1-0716-3226-0_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Meiosis is a very essential cell division resulting in the formation of four haploid gametes in plants. The preparation of meiotic chromosomes is a key step in plant meiotic research. Well-spread chromosomes, low background signal, and effective cell wall elimination give the best hybridization results. Dogroses (Rosa, section Caninae) are allopolyploids and frequently pentaploids (2n = 5x = 35) with asymmetrical meiosis. Their cytoplasm is enriched with organic compounds such as vitamins, tannins, phenols, essential oils, and many more. The cytoplasm is often a huge problem, avoiding successful cytogenetic experiments using fluorescence staining techniques. Here, we present a protocol with modifications for the preparation of male meiotic chromosomes suitable for fluorescence in situ hybridization (FISH) and immunolabeling with a major focus on dogroses.
Collapse
Affiliation(s)
- Jana Lunerová
- Department of Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská, Brno, Czech Republic.
| | - Radka Vozárová
- Department of Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská, Brno, Czech Republic
| |
Collapse
|
|
5
|
Herklotz V, Kovařík A, Wissemann V, Lunerová J, Vozárová R, Buschmann S, Olbricht K, Groth M, Ritz CM. Power and Weakness of Repetition - Evaluating the Phylogenetic Signal From Repeatomes in the Family Rosaceae With Two Case Studies From Genera Prone to Polyploidy and Hybridization ( Rosa and Fragaria). FRONTIERS IN PLANT SCIENCE 2021; 12:738119. [PMID: 34950159 PMCID: PMC8688825 DOI: 10.3389/fpls.2021.738119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Plant genomes consist, to a considerable extent, of non-coding repetitive DNA. Several studies showed that phylogenetic signals can be extracted from such repeatome data by using among-species dissimilarities from the RepeatExplorer2 pipeline as distance measures. Here, we advanced this approach by adjusting the read input for comparative clustering indirectly proportional to genome size and by summarizing all clusters into a main distance matrix subjected to Neighbor Joining algorithms and Principal Coordinate Analyses. Thus, our multivariate statistical method works as a "repeatomic fingerprint," and we proved its power and limitations by exemplarily applying it to the family Rosaceae at intrafamilial and, in the genera Fragaria and Rosa, at the intrageneric level. Since both taxa are prone to hybridization events, we wanted to show whether repeatome data are suitable to unravel the origin of natural and synthetic hybrids. In addition, we compared the results based on complete repeatomes with those from ribosomal DNA clusters only, because they represent one of the most widely used barcoding markers. Our results demonstrated that repeatome data contained a clear phylogenetic signal supporting the current subfamilial classification within Rosaceae. Accordingly, the well-accepted major evolutionary lineages within Fragaria were distinguished, and hybrids showed intermediate positions between parental species in data sets retrieved from both complete repeatomes and rDNA clusters. Within the taxonomically more complicated and particularly frequently hybridizing genus Rosa, we detected rather weak phylogenetic signals but surprisingly found a geographic pattern at a population scale. In sum, our method revealed promising results at larger taxonomic scales as well as within taxa with manageable levels of reticulation, but success remained rather taxon specific. Since repeatomes can be technically easy and comparably inexpensively retrieved even from samples of rather poor DNA quality, our phylogenomic method serves as a valuable alternative when high-quality genomes are unavailable, for example, in the case of old museum specimens.
Collapse
Affiliation(s)
- Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Volker Wissemann
- Institute of Botany, Systematic Botany Group, Justus-Liebig-University, Gießen, Germany
| | - Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Radka Vozárová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Sebastian Buschmann
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | | | - Marco Groth
- CF DNA Sequencing, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Christiane M. Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Chair of Biodiversity of Higher Plants, Technische Universität Dresden, International Institute (IHI) Zittau, Zittau, Germany
| |
Collapse
|
|
6
|
Vozárová R, Herklotz V, Kovařík A, Tynkevich YO, Volkov RA, Ritz CM, Lunerová J. Ancient Origin of Two 5S rDNA Families Dominating in the Genus Rosa and Their Behavior in the Canina-Type Meiosis. FRONTIERS IN PLANT SCIENCE 2021; 12:643548. [PMID: 33763100 PMCID: PMC7984461 DOI: 10.3389/fpls.2021.643548] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/15/2021] [Indexed: 05/02/2023]
Abstract
The genus Rosa comprises more than 100 woody species characterized by intensive hybridization, introgression, and an overall complex evolutionary history. Besides many diploid species (2n = 2x = 14) polyploids ranging from 3x to 10x are frequently found. Here we analyzed 5S ribosomal DNA in 19 species covering two subgenera and the major sections within subg. Rosa. In addition to diploids and polyploids with regular meiosis, we focused on 5x dogroses (Rosa sect. Caninae), which exhibit an asymmetric meiosis differentiating between bivalent- and univalent-forming chromosomes. Using genomic resources, we reconstructed 5S rDNA units to reveal their phylogenetic relationships. Additionally, we designed locus-specific probes derived from intergenic spacers (IGSs) and determined the position and number of 5S rDNA families on chromosomes. Two major 5S rDNA families (termed 5S_A and 5S_B, respectively) were found at variable ratios in both diploid and polyploid species including members of the early diverging subgenera, Rosa persica and Rosa minutifolia. Within subg. Rosa species of sect. Rosa amplified the 5S_A variant only, while taxa of other sections contained both variants at variable ratios. The 5S_B family was often co-localized with 35S rDNA at the nucleolar organizer regions (NOR) chromosomes, whereas the co-localization of the 5S_A family with NOR was only exceptionally observed. The allo-pentaploid dogroses showed a distinct distribution of 5S rDNA families between bivalent- and univalent-forming chromosomes. In conclusion, two divergent 5S rDNA families dominate rose genomes. Both gene families apparently arose in the early history of the genus, already 30 myrs ago, and apparently survived numerous speciation events thereafter. These observations are consistent with a relatively slow genome turnover in the Rosa genus.
Collapse
Affiliation(s)
- Radka Vozárová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Yuri O. Tynkevich
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Roman A. Volkov
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Christiane M. Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Chair of Biodiversity of Higher Plants, International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany
| | - Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| |
Collapse
|
|
7
|
Lunerová J, Herklotz V, Laudien M, Vozárová R, Groth M, Kovařík A, Ritz CM. Asymmetrical canina meiosis is accompanied by the expansion of a pericentromeric satellite in non-recombining univalent chromosomes in the genus Rosa. ANNALS OF BOTANY 2020; 125:1025-1038. [PMID: 32095807 PMCID: PMC7262465 DOI: 10.1093/aob/mcaa028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 02/24/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Despite their abundant odd-ploidy (2n = 5x = 35), dogroses (Rosa sect. Caninae) are capable of sexual reproduction due to their unique meiosis. During canina meiosis, two sets of chromosomes form bivalents and are transmitted by male and female gametes, whereas the remaining chromosomes form univalents and are exclusively transmitted by the egg cells. Thus, the evolution of chromosomes is expected to be driven by their behaviour during meiosis. METHODS To gain insight into differential chromosome evolution, fluorescence in situ hybridization was conducted for mitotic and meiotic chromosomes in four dogroses (two subsections) using satellite and ribosomal DNA probes. By exploiting high-throughput sequencing data, we determined the abundance and diversity of the satellite repeats in the genus Rosa by analysing 20 pentaploid, tetraploid and diploid species in total. KEY RESULTS A pericentromeric satellite repeat, CANR4, was found in all members of the genus Rosa, including the basal subgenera Hulthemia and Hesperhodos. The satellite was distributed across multiple chromosomes (5-20 sites per mitotic cell), and its genomic abundance was higher in pentaploid dogroses (2.3 %) than in non-dogrose species (1.3 %). In dogrose meiosis, univalent chromosomes were markedly enriched in CANR4 repeats based on both the number and the intensity of the signals compared to bivalent-forming chromosomes. Single-nucleotide polymorphisms and cluster analysis revealed high intragenomic homogeneity of the satellite in dogrose genomes. CONCLUSIONS The CANR4 satellite arose early in the evolution of the genus Rosa. Its high content and extraordinary homogeneity in dogrose genomes is explained by its recent amplification in non-recombining chromosomes. We hypothesize that satellite DNA expansion may contribute to the divergence of univalent chromosomes in Rosa species with non-symmetrical meiosis.
Collapse
Affiliation(s)
- Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Melanie Laudien
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Technical University Dresden, International Institute Zittau (IHI), Chair of Biodiversity of Higher Plants, Zittau, Germany
| | - Radka Vozárová
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
- Masaryk University, Faculty of Science, Brno, Czech Republic
| | - Marco Groth
- Leibniz Institute on Ageing – Fritz Lipmann Institute, Jena, Germany
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Christiane M Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| |
Collapse
|
|
8
|
Wilkinson MJ. The love life of a rose. A commentary on: 'Asymmetrical canina meiosis is accompanied by the expansion of a pericentric satellite in non-recombining univalent chromosomes'. ANNALS OF BOTANY 2020; 125:v-vi. [PMID: 32476016 PMCID: PMC7262460 DOI: 10.1093/aob/mcaa075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This article comments on: Jana Lunerová, Veit Herklotz, Melanie Laudien, Radka Vozárová, Marco Groth, Aleš Kovařík and Christiane M. Ritz, Asymmetrical canina meiosis is accompanied by the expansion of a pericentromeric satellite in non-recombining univalent chromosomes in the genus Rosa, Annals of Botany, Volume 125, Issue 7, 4 June 2020, Pages 1025–1038, https://doi.org/10.1093/aob/mcaa028
Collapse
Affiliation(s)
- Mike J Wilkinson
- Institute of Biological Environmental and Rural Sciences, University of Aberystwyth, Ceredigion, Wales, UK
| |
Collapse
|
|
9
|
Rovná K, Ivanišová E, Žiarovská J, Ferus P, Terentjeva M, Kowalczewski PŁ, Kačániová M. Characterization of Rosa canina Fruits Collected in Urban Areas of Slovakia. Genome Size, iPBS Profiles and Antioxidant and Antimicrobial Activities. Molecules 2020; 25:E1888. [PMID: 32325812 PMCID: PMC7221986 DOI: 10.3390/molecules25081888] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/13/2020] [Accepted: 04/17/2020] [Indexed: 11/17/2022] Open
Abstract
The studies of plant bacterial endophytes, colonizing the plant tissues without any signs of diseases, are essential for understanding of ecological interactions. The aim of our study is to detect microbiological contamination and to assess the antimicrobial, antioxidant activity, total phenolic, carotenoid content, genome size, and ploidy of non-cultivated Rosa canina sampled from urban areas. Samples of Rosa canina fruits were collected in three locations in Slovakia. The highest total viable count and the Enterobacteriaceae count in fruits were 4.32 log CFU/g and 4.29 log CFU/g, respectively. Counts of the mesophilic anaerobic sporulating bacteria, Pseudomonas spp., and of the microscopic fungi and yeasts were 3.00, 2.15 log CFU/g, 3.65 log CFU/g, and 2.76 log CFU/g, respectively. Regarding the antimicrobial activity, Escherichia coli and Klebsiela oxytoca were the most sensitive species among the assayed microorganisms to the treatment with the ethanolic extracts of Rosa canina fruits. The fruits were rich in bioactive compounds, polyphenols, and carotenoids, that could be related to their antioxidant activity. Genome sizes of analyzed samples ranged from 2.3 to 2.96. DNA-based fingerprinting obtained by iPBS markers of the Rosa canina var. lapidicola Heinr. Braun., was characterized by some distinctive inserted loci. An interdisciplinary study was performed for the dog roses from different parts of Slovakia that resulted in deeper characterization of this species.
Collapse
Affiliation(s)
- Katarína Rovná
- Department of Planting Design and Maintenance, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Tr. A. Hlinku 2, 94976 Nitra, Slovakia;
| | - Eva Ivanišová
- Department of Technology and Quality of Plant Products, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture, Tr. A. Hlinku 2, SK-94976 Nitra, Slovakia;
| | - Jana Žiarovská
- Department of Plant Genetics and Breeding, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, Tr. A. Hlinku 2, 94976 Nitra, Slovakia;
| | - Peter Ferus
- Department of Dendrobiology, Institute of Forest Ecology, Slovak Academy of Sciences, Ľ. Štúra 2, 96053 Zvolen, Slovakia;
| | - Margarita Terentjeva
- Institute of Food and Environmental Hygiene, Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, K. Helmaņaiela 8, LV-3004, Jelgava, Latvia;
| | - Przemysław Łukasz Kowalczewski
- Institute of Food Technology of Plant Origin, Poznań University of Life Sciences, 31 Wojska Polskiego St., 60-624 Poznań, Poland;
| | - Miroslava Kačániová
- Department of Fruit Sciences, Viticulture and Enology, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
- Department of Bioenergy, Food Technology and Microbiology, Institute of Agriculture Sciences, Land Management and Environmental Protection, University of Rzeszow, 4 Zelwerowicza St., 35601 Rzeszow, Poland
| |
Collapse
|
|
10
|
Smulders MJM, Arens P, Bourke PM, Debener T, Linde M, Riek JD, Leus L, Ruttink T, Baudino S, Hibrant Saint-Oyant L, Clotault J, Foucher F. In the name of the rose: a roadmap for rose research in the genome era. HORTICULTURE RESEARCH 2019; 6:65. [PMID: 31069087 PMCID: PMC6499834 DOI: 10.1038/s41438-019-0156-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/18/2019] [Indexed: 05/07/2023]
Abstract
The recent completion of the rose genome sequence is not the end of a process, but rather a starting point that opens up a whole set of new and exciting activities. Next to a high-quality genome sequence other genomic tools have also become available for rose, including transcriptomics data, a high-density single-nucleotide polymorphism array and software to perform linkage and quantitative trait locus mapping in polyploids. Rose cultivars are highly heterogeneous and diverse. This vast diversity in cultivated roses can be explained through the genetic potential of the genus, introgressions from wild species into commercial tetraploid germplasm and the inimitable efforts of historical breeders. We can now investigate how this diversity can best be exploited and refined in future breeding work, given the rich molecular toolbox now available to the rose breeding community. This paper presents possible lines of research now that rose has entered the genomics era, and attempts to partially answer the question that arises after the completion of any draft genome sequence: 'Now that we have "the" genome, what's next?'. Having access to a genome sequence will allow both (fundamental) scientific and (applied) breeding-orientated questions to be addressed. We outline possible approaches for a number of these questions.
Collapse
Affiliation(s)
- Marinus J. M. Smulders
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Paul Arens
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Peter M. Bourke
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Thomas Debener
- Faculty of Natural Sciences, Institute for Plant Genetics, Molecular Plant Breeding, Leibniz University of Hannover, Herrenhäuser Strasse 2, 30419 Hannover, Germany
| | - Marcus Linde
- Faculty of Natural Sciences, Institute for Plant Genetics, Molecular Plant Breeding, Leibniz University of Hannover, Herrenhäuser Strasse 2, 30419 Hannover, Germany
| | - Jan De Riek
- ILVO, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Caritasstraat 39, 9090 Melle, Belgium
| | - Leen Leus
- ILVO, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Caritasstraat 39, 9090 Melle, Belgium
| | - Tom Ruttink
- ILVO, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Caritasstraat 39, 9090 Melle, Belgium
| | - Sylvie Baudino
- BVpam CNRS, FRE 3727, UJM-Saint-Étienne, Univ. Lyon, Saint-Etienne, France
| | - Laurence Hibrant Saint-Oyant
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, SFR 4207 QuaSaV, 42 rue Georges Morel BP 60057, 49 071 Beaucouzé, France
| | - Jeremy Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, SFR 4207 QuaSaV, 42 rue Georges Morel BP 60057, 49 071 Beaucouzé, France
| | - Fabrice Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, SFR 4207 QuaSaV, 42 rue Georges Morel BP 60057, 49 071 Beaucouzé, France
| |
Collapse
|
|
11
|
Kolarčik V, Kocová V, Vašková D. Flow cytometric seed screen data are consistent with models of chromosome inheritance in asymmetrically compensating allopolyploids. Cytometry A 2018; 93:737-748. [PMID: 30071155 DOI: 10.1002/cyto.a.23511] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 05/10/2018] [Accepted: 06/04/2018] [Indexed: 12/19/2022]
Abstract
Angiosperms have evolved a mechanism of double fertilization, which results in the production of a separate embryo (new individual) and endosperm (nutritive tissue). The flow cytometric seed screen (FCSS) was developed to infer plant reproduction modes based on endosperm-to-embryo DNA content ratio (Pind ). A ratio of 1.5 indicates sexual reproduction, whereas higher values of ≥2.0 are consistent with apomixis. Although FCSS has been successfully applied to the study of sexual and asexual plants, the limits of FCSS and particularly its potential for determination of reproduction modes in hemisexual plants have not been explored. Here, we evaluated the application of FCSS to the study of reproduction modes in two asymmetrically compensating allopolyploids (ACAs), Onosma arenaria and Rosa canina. These two species are characterized by the presence of asexually inherited univalent-forming and sexually inherited bivalent-forming chromosome sets. They both use asymmetric meiosis, which eliminates univalent-forming chromosome sets from the male gamete and retains them in the female gamete. Different chromosomal behavior in male and female meiosis in these plants is reflected in different theoretically derived Pind values, which deviate from a sexual 1.5 value. Here, we determined Pind FCSS-based values in seeds of ACAs, and compared the results to sexual species. As expected, we determined that the mean Pind is 1.51, 1.52, and 1.52 in the sexual plants, that is, Capsella bursa-pastoris, Crataegus monogyna, and O. pseudoarenaria, respectively. In the ACAs, different mean Pind values were determined for O. arenaria (1.61) and R. canina (1.82). These values are consistent with the theoretical Pind values determined based on models of chromosome inheritance. This study highlights the precision of flow cytometry in determining DNA content and it's utility in screening reproduction modes. Additionally, it advocates for more in-depth investigations into rapid screening of accessions where the Pind ratio has deviated from the 1.5 value typical of sexual species, which may indicate meiotic irregularities.
Collapse
Affiliation(s)
- V Kolarčik
- Department of Botany, Institute of Biology and Ecology, Faculty of Science, P. J. Šafárik University, Mánesova 23, SK-041 54, Košice, Slovak Republic
| | - V Kocová
- Department of Botany, Institute of Biology and Ecology, Faculty of Science, P. J. Šafárik University, Mánesova 23, SK-041 54, Košice, Slovak Republic
| | - D Vašková
- Department of Botany, Institute of Biology and Ecology, Faculty of Science, P. J. Šafárik University, Mánesova 23, SK-041 54, Košice, Slovak Republic
| |
Collapse
|
|
12
|
Herklotz V, Kovařík A, Lunerová J, Lippitsch S, Groth M, Ritz CM. The fate of ribosomal RNA genes in spontaneous polyploid dogrose hybrids [Rosa L. sect. Caninae (DC.) Ser.] exhibiting non-symmetrical meiosis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:77-90. [PMID: 29385286 DOI: 10.1111/tpj.13843] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 01/03/2018] [Accepted: 01/15/2018] [Indexed: 05/02/2023]
Abstract
Dogroses represent an exceptional system for studying the effects of genome doubling and hybridization: their asymmetrical meiosis enables recombination in bi-parentally inherited chromosomes but prevents it in maternally inherited ones. We employed fluorescent in situ hybridization, genome skimming, amplicon sequencing of genomic and cDNA as well as conventional cloning of nuclear ribosomal DNA in two phylogenetically distinct pentaploid (2n = 5x = 35) species, Rosa canina and Rosa inodora, and their naturally occurring reciprocal hybrids, Rosa dumalis (5x) and Rosa agrestis (5x, 6x). Both progenitor species differed in composition, meiotic behaviour and expression of rDNA loci: R. canina (five 18S and 5-8 5S loci) was dominated by the Canina ribotypes, but R. inodora (four 18S loci and 7-8 5S loci) by the Rubiginosa ribotype. The co-localized 5S/18S loci occurred on either bivalent-forming (R. canina) or univalent-forming (R. inodora) chromosomes. Ribosomal DNA loci were additively inherited; however, the Canina ribotypes were dominantly expressed, even in genotypes with relatively low copy number of these genes. Moreover, we observed rDNA homogenization towards the paternally transmitted Canina ribotype in 6x R. agrestis. The here-observed variation in arrangement and composition of rDNA types between R. canina and R. inodora suggests the involvement of different genomes in bivalent formation. This results supports the hypothesis that the asymmetrical meiosis arose at least twice by independent ancient hybridization events.
Collapse
Affiliation(s)
- Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Am Museum 1, D-02826, Görlitz, Germany
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Susan Lippitsch
- Department of Ecology and Environment Protection, University of Applied Sciences Zittau/Görlitz, Theodor-Körner-Allee 16, D-02763, Zittau, Germany
| | - Marco Groth
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745, Jena, Germany
| | - Christiane M Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Am Museum 1, D-02826, Görlitz, Germany
| |
Collapse
|
|
13
|
Lenormand T, Engelstädter J, Johnston SE, Wijnker E, Haag CR. Evolutionary mysteries in meiosis. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2016.0001. [PMID: 27619705 DOI: 10.1098/rstb.2016.0001] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2016] [Indexed: 01/25/2023] Open
Abstract
Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these often 'weird' features. We discuss the origin of meiosis (origin of ploidy reduction and recombination, two-step meiosis), its secondary modifications (in polyploids or asexuals, inverted meiosis), its importance in punctuating life cycles (meiotic arrests, epigenetic resetting, meiotic asymmetry, meiotic fairness) and features associated with recombination (disjunction constraints, heterochiasmy, crossover interference and hotspots). We present the various evolutionary scenarios and selective pressures that have been proposed to account for these features, and we highlight that their evolutionary significance often remains largely mysterious. Resolving these mysteries will likely provide decisive steps towards understanding why sex and recombination are found in the majority of eukaryotes.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.
Collapse
Affiliation(s)
- Thomas Lenormand
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier-Université Paul-Valéry Montpellier-Ecole Pratique des Hautes Etudes (EPHE), 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Erik Wijnker
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Christoph R Haag
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier-Université Paul-Valéry Montpellier-Ecole Pratique des Hautes Etudes (EPHE), 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| |
Collapse
|
|
14
|
Kirov IV, Van Laere K, Van Roy N, Khrustaleva LI. Towards a FISH-based karyotype of Rosa L. (Rosaceae). COMPARATIVE CYTOGENETICS 2016; 10:543-554. [PMID: 28123677 PMCID: PMC5240508 DOI: 10.3897/compcytogen.v10i4.9536] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/08/2016] [Indexed: 05/18/2023]
Abstract
The genus Rosa Linnaeus, 1753 has important economic value in ornamental sector and many breeding activities are going on supported by molecular studies. However, the cytogenetic studies of rose species are scarce and mainly focused on chromosome counting and chromosome morphology-based karyotyping. Due to the small size of the chromosomes and a high frequency of polyploidy in the genus, karyotyping is very challenging for rose species and requires FISH-based cytogenetic markers to be applied. Therefore, in this work the aim is to establish a FISH-based karyotype for Rosa wichurana (Crépin, 1888), a rose species with several benefits for advanced molecular cytogenetic studies of genus Rosa (Kirov et al. 2015a). It is shown that FISH signals from 5S, 45S and an Arabidopsis-type telomeric repeat are distributed on five (1, 2, 4, 5 and 7) of seven chromosome pairs. In addition, it is demonstrated that the interstitial telomeric repeat sequences (ITR) are located in the centromeric regions of four chromosome pairs. Using low hybridization stringency for ITR visualization, we showed that the number of ITR signals increases four times (1-4 signals). This study is the first to propose a FISH-based Rosa wichurana karyotype for the reliable identification of chromosomes. The possible origin of Rosa wichurana ITR loci is discussed.
Collapse
Affiliation(s)
- Ilya V. Kirov
- Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str. 49, 127550, Moscow, Russia
- Department of Genetics and Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str. 3, 127550, Moscow, Russia
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 39, 9090, Melle, Belgium
| | - Katrijn Van Laere
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 39, 9090, Melle, Belgium
| | - Nadine Van Roy
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium
| | - Ludmila I. Khrustaleva
- Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str. 49, 127550, Moscow, Russia
- Department of Genetics and Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str. 3, 127550, Moscow, Russia
| |
Collapse
|
|
15
|
Wang Y, Wang X, Chen Q, Zhang L, Tang H, Luo Y, Liu Z. Phylogenetic insight into subgenera Idaeobatus and Malachobatus (Rubus, Rosaceae) inferring from ISH analysis. Mol Cytogenet 2015; 8:11. [PMID: 25674160 PMCID: PMC4324050 DOI: 10.1186/s13039-015-0114-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/21/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rubus is a large and taxonomically complex genus exhibiting agamospermy, polyploidy and frequent hybridization. The objective of this work was to elucidate rDNA disrtibution pattern and investigate genomic composition of polyploids in 16 Rubus taxa (2n = 2x, 3x, 4x, 8x) of two subgenera Idaeobatus and Malachobatus by ISH method. RESULTS The basic Rubus genome had one 45S rDNA locus, and all the polyploids (except R. setchuenensis) had the expected multiples of this number. Diploid and tetraploid Rubus taxa carried two 5S rDNA, whereas the triploid and octoploid species only had three. The duplicated 45S rDNA sites tended to be conserved, whereas those of 5S rDNA tended to be eliminated after polyploidization. The accession R03-20 was an autotriploid R. parvifolius, while R03-27 and R03-57 were naturally-occurred triploid hybrids between R. parvifolius and R. coreanus. GISH results suggested that R. parvifolius had close relationship with polyploids from Malachobatus. CONCLUSIONS The polyploids from Malachobatus were probable allopolyploid. In addition, Rubus parvifolius might be involved in hybridization, polyploidization and speciation of some Idaeobatus and Malachobatus species.
Collapse
Affiliation(s)
- Yan Wang
- />College of Horticulture, Sichuan Agricultural University, Ya’an, 625014 People’s Republic of China
| | - Xiaorong Wang
- />College of Horticulture, Sichuan Agricultural University, Ya’an, 625014 People’s Republic of China
- />Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130 People’s Republic of China
| | - Qing Chen
- />College of Horticulture, Sichuan Agricultural University, Ya’an, 625014 People’s Republic of China
| | - Li Zhang
- />College of Horticulture, Sichuan Agricultural University, Ya’an, 625014 People’s Republic of China
| | - Haoru Tang
- />College of Horticulture, Sichuan Agricultural University, Ya’an, 625014 People’s Republic of China
| | - Ya Luo
- />College of Horticulture, Sichuan Agricultural University, Ya’an, 625014 People’s Republic of China
| | - Zejing Liu
- />College of Horticulture, Sichuan Agricultural University, Ya’an, 625014 People’s Republic of China
| |
Collapse
|
|
16
|
Fougère-Danezan M, Joly S, Bruneau A, Gao XF, Zhang LB. Phylogeny and biogeography of wild roses with specific attention to polyploids. ANNALS OF BOTANY 2015; 115:275-91. [PMID: 25550144 PMCID: PMC4551085 DOI: 10.1093/aob/mcu245] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 09/15/2014] [Accepted: 10/27/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS The genus Rosa (150-200 species) is widely distributed throughout temperate and sub-tropical habitats from the northern hemisphere to tropical Asia, with only one tropical African species. In order to better understand the evolution of roses, this study examines infrageneric relationships with respect to conventional taxonomy, considers the extent of allopolyploidization and infers macroevolutionary processes that have led to the current distribution of the genus. METHODS Phylogenetic relationships among 101 species of the genus Rosa were reconstructed using sequences from the plastid psbA-trnH spacer, trnL intron, trnL-F spacer, trnS-G spacer and trnG intron, as well as from nuclear glyceraldehyde 3-phosphate dehydrogenase (GAPDH), which was used to identify putative allopolyploids and infer their possible origins. Chloroplast phylogeny was used to estimate divergence times and reconstruct ancestral areas. KEY RESULTS Most subgenera and sections defined by traditional taxonomy are not monophyletic. However, several clades are partly consistent with currently recognized sections. Allopolyploidy seems to have played an important role in stabilizing intersectional hybrids. Biogeographic analyses suggest that Asia played a central role as a genetic reservoir in the evolution of the genus Rosa. CONCLUSIONS The ancestral area reconstruction suggests that despite an early presence on the American continent, most extant American species are the results of a later re-colonization from Asia, probably through the Bering Land Bridge. The results suggest more recent exchanges between Asia and western North America than with eastern North America. The current distribution of roses from the Synstylae lineage in Europe is probably the result of a migration from Asia approx. 30 million years ago, after the closure of the Turgai strait. Directions for a new sectional classification of the genus Rosa are proposed, and the analyses provide an evolutionary framework for future studies on this notoriously difficult genus.
Collapse
Affiliation(s)
- Marie Fougère-Danezan
- Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu, Sichuan 610041, China, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China, Institut de Recherche en Biologie Végétale (Département de Sciences biologiques), Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada, Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada and Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299, USA Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu, Sichuan 610041, China, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China, Institut de Recherche en Biologie Végétale (Département de Sciences biologiques), Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada, Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada and Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299, USA
| | - Simon Joly
- Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu, Sichuan 610041, China, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China, Institut de Recherche en Biologie Végétale (Département de Sciences biologiques), Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada, Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada and Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299, USA Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu, Sichuan 610041, China, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China, Institut de Recherche en Biologie Végétale (Département de Sciences biologiques), Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada, Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada and Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299, USA
| | - Anne Bruneau
- Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu, Sichuan 610041, China, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China, Institut de Recherche en Biologie Végétale (Département de Sciences biologiques), Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada, Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada and Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299, USA
| | - Xin-Fen Gao
- Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu, Sichuan 610041, China, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China, Institut de Recherche en Biologie Végétale (Département de Sciences biologiques), Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada, Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada and Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299, USA
| | - Li-Bing Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu, Sichuan 610041, China, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China, Institut de Recherche en Biologie Végétale (Département de Sciences biologiques), Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada, Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada and Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299, USA Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu, Sichuan 610041, China, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China, Institut de Recherche en Biologie Végétale (Département de Sciences biologiques), Université de Montréal, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada, Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, Québec H1X 2B2, Canada and Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299, USA
| |
Collapse
|
|
17
|
Kolarčik V, Zozomová-Lihová J, Ducár E, Mártonfi P. Evolutionary significance of hybridization inOnosma(Boraginaceae): analyses of stabilized hemisexual odd polyploids and recent sterile hybrids. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12270] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Vladislav Kolarčik
- Institute of Biology and Ecology; Faculty of Science; P. J. Šafárik University; Mánesova 23 Košice SK-041 54 Slovak Republic
| | - Judita Zozomová-Lihová
- Institute of Botany; Slovak Academy of Sciences; Dúbravská cesta 9 Bratislava SK-845 23 Slovak Republic
| | - Erik Ducár
- Institute of Biology and Ecology; Faculty of Science; P. J. Šafárik University; Mánesova 23 Košice SK-041 54 Slovak Republic
| | - Pavol Mártonfi
- Institute of Biology and Ecology; Faculty of Science; P. J. Šafárik University; Mánesova 23 Košice SK-041 54 Slovak Republic
| |
Collapse
|
|
18
|
Crhak Khaitova L, Werlemark G, Kovarikova A, Nybom H, Kovarik A. High penetrance of a pan-canina type rDNA family in intersection Rosa hybrids suggests strong selection of bivalent chromosomes in the section Caninae. Cytogenet Genome Res 2014; 143:104-13. [PMID: 24685720 DOI: 10.1159/000360437] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
All dogroses (Rosa sect. Caninae) are characterized by the peculiar canina meiosis in which genetic material is unevenly distributed between female and male gametes. The pan-canina rDNA family (termed beta) appears to be conserved in all dogroses analyzed so far. Here, we have studied rDNAs in experimental hybrids obtained from open pollination of F1 plants derived from 2 independent intersectional crosses between the pentaploid dogrose species (2n = 5x = 35) Rosa rubiginosa as female parent (producing 4x egg cells due to the unique asymmetrical canina meiosis) and the tetraploid (2n = 4x = 28) garden rose R. hybrida 'André Brichet' as male parent (producing 2x pollen after normal meiosis). We analyzed the structure of rDNA units by molecular methods [CAPS and extensive sequencing of internal transcribed spacers (ITS)] and determined the number of loci on chromosomes by FISH. FISH showed that R. rubiginosa and 'André Brichet' harbored 5 and 4 highly heteromorphic rDNA loci, respectively. In the second generation of hybrid lines, we observed a reduced number of loci (4 and 5 instead of the expected 6). In R. rubiginosa and 'André Brichet', 2-3 major ITS types were found which is consistent with a weak homogenization pressure maintaining high diversity of ITS types in this genus. In contrast to expectation (the null hypothesis of Mendelian inheritance of ITS families), we observed reduced ITS diversity in some individuals of the second generation which might derive from self-fertilization or from a backcross to R. rubiginosa. In these individuals, the pan-canina beta family appeared to be markedly enriched, while the paternal families were lost or diminished in copies. Although the mechanism of biased meiotic transmission of certain rDNA types is currently unknown, we speculate that the bivalent-forming chromosomes carrying the beta rDNA family exhibit extraordinary pairing efficiency and/or are subjected to strong selection in Caninae polyploids.
Collapse
Affiliation(s)
- Lucie Crhak Khaitova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | | | | | | | | |
Collapse
|
|
19
|
|
|
20
|
Fredotović Ž, Šamanić I, Weiss-Schneeweiss H, Kamenjarin J, Jang TS, Puizina J. Triparental origin of triploid onion, Allium × cornutum (Clementi ex Visiani, 1842), as evidenced by molecular, phylogenetic and cytogenetic analyses. BMC PLANT BIOLOGY 2014; 14:24. [PMID: 24418109 PMCID: PMC3899691 DOI: 10.1186/1471-2229-14-24] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 01/08/2014] [Indexed: 05/09/2023]
Abstract
BACKGROUND Reconstruction of the parental origins of cultivated plants from wild relatives, especially after long periods of domestication, is not a trivial task. However, recent advances in molecular phylogenetics, among other approaches, have proved to be very informative in analyses of the origin and evolution of polyploid genomes. An established minor garden crop, triploid onion Allium × cornutum (Clementi ex Visiani, 1842) (2n = 3x = 24), is widespread in southeastern Asia and Europe. Our previous cytogenetic analyses confirmed its highly heterozygous karyotype and indicated its possible complex triparental genome origin. Allium cepa L. and Allium roylei Stearn were suggested as two putative parental species of A. × cornutum, whereas the third parental species remained hitherto unknown. RESULTS Here we report the phylogenetic analyses of the internal transcribed spacers ITS1-5.8S-ITS2 of 35S rDNA and the non-transcribed spacer (NTS) region of 5S rDNA of A. × cornutum and its relatives of the section Cepa. Both ITS and NTS sequence data revealed intra-individual variation in triploid onion, and these data clustered into the three main clades, each with high sequence homology to one of three other species of section Cepa: A. cepa, A. roylei, and unexpectedly, the wild Asian species Allium pskemense B. Fedtsh. Allium pskemense is therefore inferred to be the third, so far unknown, putative parental species of triploid onion Allium × cornutum. The 35S and 5S rRNA genes were found to be localised on somatic chromosomes of A. × cornutum and its putative parental species by double fluorescent in situ hybridisation (FISH). The localisation of 35S and 5S rDNA in A. × cornutum chromosomes corresponded to their respective positions in the three putative parental species, A. cepa, A. pskemense, and A. roylei. GISH (genomic in situ hybridisation) using DNA of the three putative parental diploids corroborated the results of the phylogenetic study. CONCLUSIONS The combined molecular, phylogenetic and cytogenetic data obtained in this study provided evidence for a unique triparental origin of triploid onion A. × cornutum with three putative parental species, A. cepa, A. pskemense, and A. roylei.
Collapse
Affiliation(s)
- Željana Fredotović
- Department of Biology, University of Split, Faculty of Science, Teslina 12, 21000 Split, Croatia
| | - Ivica Šamanić
- Department of Biology, University of Split, Faculty of Science, Teslina 12, 21000 Split, Croatia
| | - Hanna Weiss-Schneeweiss
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Juraj Kamenjarin
- Department of Biology, University of Split, Faculty of Science, Teslina 12, 21000 Split, Croatia
| | - Tae-Soo Jang
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Jasna Puizina
- Department of Biology, University of Split, Faculty of Science, Teslina 12, 21000 Split, Croatia
| |
Collapse
|
|
21
|
Grandont L, Jenczewski E, Lloyd A. Meiosis and its deviations in polyploid plants. Cytogenet Genome Res 2013; 140:171-84. [PMID: 23817089 DOI: 10.1159/000351730] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Meiosis is a fundamental process in all sexual organisms that ensures fertility and genome stability and creates genetic diversity. For each of these outcomes, the exclusive formation of crossovers between homologous chromosomes is needed. This is more difficult to achieve in polyploid species which have more than 2 sets of chromosomes able to recombine. In this review, we describe how meiosis and meiotic recombination 'deviate' in polyploid plants compared to diploids, and give an overview of current knowledge on how they are regulated. See also the sister article focusing on animals by Stenberg and Saura in this themed issue.
Collapse
Affiliation(s)
- L Grandont
- INRA - Institut Jean Pierre Bourgin, Station de Génétique et Amélioration des Plantes, Versailles, France
| | | | | |
Collapse
|
|
22
|
De Riek J, De Cock K, Smulders MJM, Nybom H. AFLP-based population structure analysis as a means to validate the complex taxonomy of dogroses (Rosa section Caninae). Mol Phylogenet Evol 2013; 67:547-59. [PMID: 23499615 DOI: 10.1016/j.ympev.2013.02.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 02/07/2013] [Accepted: 02/25/2013] [Indexed: 01/17/2023]
Abstract
Within the genus Rosa numerous species have been described. Circumscription of the dogrose section Caninae is straightforward, but the delineation of species and subsections within this section is less clear, partly due to hybridisation between species. We have investigated the extent to which DNA marker-based information of wild populations corroborates present-day dogrose taxonomy and hypotheses about the origination of taxa. Sampling was conducted in a transect across Europe, collecting over 900 specimens of all encountered dogrose taxa. For comparison, we also included more than 200 samples of species belonging to other sections. Two lines of statistical analyses were used to investigate the genetic structure based on AFLP data: (1) an unstructured model with principal coordinate analysis and hierarchical clustering, and (2) a model with a superimposed taxonomic structure based on analysis of genetic diversity using a novel approach combining assignment tests with canonical discriminant analysis. Support was found for five of the seven subsections, whereas R. balsamica apparently belongs to subsection Caninae thus omitting the need for recognising subsection Tomentellae. For R. stylosa, a hybridogenic origin with a non-dogrose section member has been suggested, and it can be treated either as a separate subsection or within subsection Caninae. Within the subsection Rubigineae, a species cluster with low support for the taxa R. micrantha, R. rubiginosa and the putatively hybridogenous R. gremlii was identified. Similarly, several species in the subsection Caninae overlapped considerably, and are best regarded as one common species complex. This population genetic approach provides a general method to validate the taxonomic system in complex and polyploid taxa.
Collapse
Affiliation(s)
- Jan De Riek
- Institute for Agricultural and Fisheries Research, Plant Sciences Unit - Applied Genetics and Breeding, Caritasstraat 21, 9090 Melle, Belgium.
| | | | | | | |
Collapse
|
|
23
|
Bendahmane M, Dubois A, Raymond O, Bris ML. Genetics and genomics of flower initiation and development in roses. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:847-57. [PMID: 23364936 PMCID: PMC3594942 DOI: 10.1093/jxb/ers387] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Roses hold high symbolic value and great cultural importance in different societies throughout human history. They are widely used as garden ornamental plants, as cut flowers, and for the production of essential oils for the perfume and cosmetic industries. Domestication of roses has a long and complex history, and the rose species have been hybridized across vast geographic areas such as Europe, Asia, and the Middle East. The domestication processes selected several flower characters affecting floral quality, such as recurrent flowering, double flowers, petal colours, and fragrance. The molecular and genetic events that determine some of these flower characters cannot be studied using model species such as Arabidopsis thaliana, or at least only in a limited manner. In this review, we comment on the recent development of genetic, genomic, and transcriptomic tools for roses, and then focus on recent advances that have helped unravel the molecular mechanisms underlying several rose floral traits.
Collapse
Affiliation(s)
- Mohammed Bendahmane
- Reproduction et Développement des Plantes UMR INRA-CNRS-Université Lyon 1-ENSL, IFR128 BioSciences-Gerland Lyon sud, Ecole Normale Supérieure, 46 allée d'Italie, Lyon Cedex 07, France.
| | | | | | | |
Collapse
|
|
24
|
Matyášek R, Renny-Byfield S, Fulneček J, Macas J, Grandbastien MA, Nichols R, Leitch A, Kovařík A. Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids. BMC Genomics 2012; 13:722. [PMID: 23259460 PMCID: PMC3563450 DOI: 10.1186/1471-2164-13-722] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 12/13/2012] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Tandemly arranged nuclear ribosomal DNA (rDNA), encoding 18S, 5.8S and 26S ribosomal RNA (rRNA), exhibit concerted evolution, a pattern thought to result from the homogenisation of rDNA arrays. However rDNA homogeneity at the single nucleotide polymorphism (SNP) level has not been detailed in organisms with more than a few hundred copies of the rDNA unit. Here we study rDNA complexity in species with arrays consisting of thousands of units. METHODS We examined homogeneity of genic (18S) and non-coding internally transcribed spacer (ITS1) regions of rDNA using Roche 454 and/or Illumina platforms in four angiosperm species, Nicotiana sylvestris, N. tomentosiformis, N. otophora and N. kawakamii. We compared the data with Southern blot hybridisation revealing the structure of intergenic spacer (IGS) sequences and with the number and distribution of rDNA loci. RESULTS AND CONCLUSIONS In all four species the intragenomic homogeneity of the 18S gene was high; a single ribotype makes up over 90% of the genes. However greater variation was observed in the ITS1 region, particularly in species with two or more rDNA loci, where >55% of rDNA units were a single ribotype, with the second most abundant variant accounted for >18% of units. IGS heterogeneity was high in all species. The increased number of ribotypes in ITS1 compared with 18S sequences may reflect rounds of incomplete homogenisation with strong selection for functional genic regions and relaxed selection on ITS1 variants. The relationship between the number of ITS1 ribotypes and the number of rDNA loci leads us to propose that rDNA evolution and complexity is influenced by locus number and/or amplification of orphaned rDNA units at new chromosomal locations.
Collapse
Affiliation(s)
- Roman Matyášek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i, Královopolská 135, Brno, CZ-612 65, Czech Republic
| | - Simon Renny-Byfield
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London, E1 4NS, UK
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Jaroslav Fulneček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i, Královopolská 135, Brno, CZ-612 65, Czech Republic
| | - Jiří Macas
- Biology Centre, Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-370 05, Czech Republic
| | - Marie-Angele Grandbastien
- Institut Jean-Pierre Bourgin, Laboratoire de Biologie Cellulaire, INRA-Centre de Versailles, Versailles Cedex, F-780 26, France
| | - Richard Nichols
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London, E1 4NS, UK
| | - Andrew Leitch
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London, E1 4NS, UK
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i, Královopolská 135, Brno, CZ-612 65, Czech Republic
| |
Collapse
|
|
25
|
Liu B, Davis TM. Conservation and loss of ribosomal RNA gene sites in diploid and polyploid Fragaria (Rosaceae). BMC PLANT BIOLOGY 2011; 11:157. [PMID: 22074487 PMCID: PMC3261831 DOI: 10.1186/1471-2229-11-157] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Accepted: 11/10/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND The genus Fragaria comprises species at ploidy levels ranging from diploid (2n = 2x = 14) to decaploid (2n = 10x = 70). Fluorescence in situ hybridization with 5S and 25S rDNA probes was performed to gather cytogenetic information that illuminates genomic divergence among different taxa at multiple ploidy levels, as well as to explore the evolution of ribosomal RNA genes during polyploidization in Fragaria. RESULTS Root tip cells of diploid taxa were typified by two 5S and six 25S rDNA hybridization signals of varying intensities, providing a baseline for comparisons within the genus. In three exceptional diploid genotypes, F. nilgerrensis (CFRA 1358 and CFRA 1825) and F. vesca 'Yellow Wonder', two 5S but only four 25S rDNA sites were found but with differing site losses. The numbers of 5S and 25S rDNA signals, respectively were three and nine in a triploid F. ×bifera accession, and were four and twelve in three tetraploids, thus occurring in proportional 1.5× and 2× multiples of the typical diploid pattern. In hexaploid F. moschata, a proportional multiple of six 5S rDNA sites was observed, but the number of 25S rDNA sites was one or two less than the proportionate prediction of eighteen. This apparent tendency toward rDNA site loss at higher ploidy was markedly expanded in octoploids, which displayed only two 5S and ten 25S rDNA sites. In the two decaploids examined, the numbers of 5S and 25S rDNA signals, respectively, were four and fifteen in F. virginiana subsp. platypetala, and six and twelve in F. iturupensis. CONCLUSIONS Among diploid Fragaria species, a general consistency of rDNA site numbers implies conserved genomic organization, but highly variable 25S signal sizes and intensities and two instances of site loss suggest concurrent high dynamics of rDNA copy numbers among both homologs and non-homologs. General conservation of rDNA site numbers in lower ploidy, but marked site number reductions at higher ploidy levels, suggest complex evolution of rDNA sites during polyploidization and/or independent evolutionary pathways for 6x versus higher ploidy strawberries. Site number comparisons suggest common genomic composition among natural octoploids, and independent origins of the two divergent decaploid accessions.
Collapse
Affiliation(s)
- Bo Liu
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Thomas M Davis
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| |
Collapse
|
|
26
|
Fukushima K, Imamura K, Nagano K, Hoshi Y. Contrasting patterns of the 5S and 45S rDNA evolutions in the Byblis liniflora complex (Byblidaceae). JOURNAL OF PLANT RESEARCH 2011; 124:231-44. [PMID: 20623155 PMCID: PMC3040357 DOI: 10.1007/s10265-010-0366-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 06/11/2010] [Indexed: 05/07/2023]
Abstract
To clarify the evolutionary dynamics of ribosomal RNA genes (rDNAs) in the Byblis liniflora complex (Byblidaceae), we investigated the 5S and 45S rDNA genes through (1) chromosomal physical mapping by fluorescence in situ hybridization (FISH) and (2) phylogenetic analyses using the nontranscribed spacer of 5S rDNA (5S-NTS) and the internal transcribed spacer of 45S rDNA (ITS). In addition, we performed phylogenetic analyses based on rbcL and trnK intron. The complex was divided into 2 clades: B. aquatica-B. filifolia and B. guehoi-B. liniflora-B. rorida. Although members of the complex had conservative symmetric karyotypes, they were clearly differentiated on chromosomal rDNA distribution patterns. The sequence data indicated that ITS was almost homogeneous in all taxa in which two or four 45S rDNA arrays were frequently found at distal regions of chromosomes in the somatic karyotype. ITS homogenization could have been prompted by relatively distal 45S rDNA positions. In contrast, 2-12 5S rDNA arrays were mapped onto proximal/interstitial regions of chromosomes, and some paralogous 5S-NTS were found in the genomes harboring 4 or more arrays. 5S-NTS sequence type-specific FISH analysis showed sequence heterogeneity within and between some 5S rDNA arrays. Interlocus homogenization may have been hampered by their proximal location on chromosomes. Chromosomal location may have affected the contrasting evolutionary dynamics of rDNAs in the B. liniflora complex.
Collapse
Affiliation(s)
- Kenji Fukushima
- Department of Basic Biology, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193 Japan
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585 Japan
| | - Kaori Imamura
- Department of Plant Science, School of Agriculture, Tokai University, Kawayou, Minamiaso-mura, Aso-gun, Kumamoto, 869-1404 Japan
- Japan Software Management Co. Ltd., 5-32 KinKou-cho, Kanagawa-ku, Yokohama, Kanagawa 221-0056 Japan
| | - Katsuya Nagano
- Department of Plant Science, School of Agriculture, Tokai University, Kawayou, Minamiaso-mura, Aso-gun, Kumamoto, 869-1404 Japan
| | - Yoshikazu Hoshi
- Department of Plant Science, School of Agriculture, Tokai University, Kawayou, Minamiaso-mura, Aso-gun, Kumamoto, 869-1404 Japan
| |
Collapse
|
|
27
|
Ritz CM, Köhnen I, Groth M, Theißen G, Wissemann V. To be or not to be the odd one out--allele-specific transcription in pentaploid dogroses (Rosa L. sect. Caninae (DC.) Ser). BMC PLANT BIOLOGY 2011; 11:37. [PMID: 21345190 PMCID: PMC3053229 DOI: 10.1186/1471-2229-11-37] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 02/23/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND Multiple hybridization events gave rise to pentaploid dogroses which can reproduce sexually despite their uneven ploidy level by the unique canina meiosis. Two homologous chromosome sets are involved in bivalent formation and are transmitted by the haploid pollen grains and the tetraploid egg cells. In addition the egg cells contain three sets of univalent chromosomes which are excluded from recombination. In this study we investigated whether differential behavior of chromosomes as bivalents or univalents is reflected by sequence divergence or transcription intensity between homeologous alleles of two single copy genes (LEAFY, cGAPDH) and one ribosomal DNA locus (nrITS). RESULTS We detected a maximum number of four different alleles of all investigated loci in pentaploid dogroses and identified the respective allele with two copies, which is presumably located on bivalent forming chromosomes. For the alleles of the ribosomal DNA locus and cGAPDH only slight, if any, differential transcription was determined, whereas the LEAFY alleles with one copy were found to be significantly stronger expressed than the LEAFY allele with two copies. Moreover, we found for the three marker genes that all alleles have been under similar regimes of purifying selection. CONCLUSIONS Analyses of both molecular sequence evolution and expression patterns did not support the hypothesis that unique alleles probably located on non-recombining chromosomes are less functional than duplicate alleles presumably located on recombining chromosomes.
Collapse
Affiliation(s)
- Christiane M Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Am Museum 1, D-02826 Görlitz, Germany
| | - Ines Köhnen
- Ziegenhainer Straße 19, D-07749 Jena, Germany
| | - Marco Groth
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstraße 11, D-07745 Jena, Germany
| | - Günter Theißen
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, D-07743 Jena, Germany
| | - Volker Wissemann
- Department of Systematic Botany, Institute of Botany, Justus Liebig University Gießen, Heinrich-Buff-Ring 38, D-35392 Gießen, Germany
| |
Collapse
|
|
28
|
Ritz CM, Wissemann V. Microsatellite analyses of artificial and spontaneous dogrose hybrids reveal the hybridogenic origin of Rosa micrantha by the contribution of unreduced gametes. ACTA ACUST UNITED AC 2011; 102:217-27. [PMID: 21220743 DOI: 10.1093/jhered/esq124] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Dogroses are characterized by a unique meiosis system, the so-called canina meiosis, which facilitates sexual reproduction at odd-number ploidy. The mostly pentaploid somatic level of dogroses is restored by a merger of haploid sperm cells and tetraploid egg cells. We analyzed experimental hybrids between different dogrose species using microsatellites to determine pollen-transmitted alleles. This information was used to reconstruct the putative hybridogenic origin of Rosa micrantha and R. dumalis and to estimate the frequency of spontaneous hybridization in a natural population. We found no evidence for the hybrid origin of R. dumalis, but our data suggest that R. micrantha presumably arose by hybridization between R. rubiginosa and R. canina or R. corymbifera. We observed only hexaploid individuals of R. micrantha, thus the establishment of this hybridogenic species was favored when unreduced gametes contributed to their origin. We demonstrate that spontaneous hybrids originated infrequently from the parental species in a natural population, but hybridization was often associated with the formation of unreduced gametes. We postulate that unreduced gametes play a major role in the evolutionary success of dogrose hybrids because they provide highly homologous chromosomes crucial for bivalent formation during canina meiosis and thus ensuring this unique form of sexual reproduction.
Collapse
Affiliation(s)
- Christiane M Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, PF 300154, D-02806 Görlitz, Germany.
| | | |
Collapse
|
|
29
|
Abstract
The first haploid angiosperm, a dwarf form of cotton with half the normal chromosome complement, was discovered in 1920, and in the ninety years since then such plants have been identified in many other species. They can occur either spontaneously or can be induced by modified pollination methods in vivo, or by in vitro culture of immature male or female gametophytes. Haploids represent an immediate, one-stage route to homozygous diploids and thence to F(1) hybrid production. The commercial exploitation of heterosis in such F(1) hybrids leads to the development of hybrid seed companies and subsequently to the GM revolution in agriculture. This review describes the range of techniques available for the isolation or induction of haploids and discusses their value in a range of areas, from fundamental research on mutant isolation and transformation, through to applied aspects of quantitative genetics and plant breeding. It will also focus on how molecular methods have been used recently to explore some of the underlying aspects of this fascinating developmental phenomenon.
Collapse
Affiliation(s)
- Jim M Dunwell
- School of Biological Sciences, University of Reading, Whiteknights, Reading, UK.
| |
Collapse
|
|
30
|
Khaitová L, Werlemark G, Nybom H, Kovarík A. Frequent silencing of rDNA loci on the univalent-forming genomes contrasts with their stable expression on the bivalent-forming genomes in polyploid dogroses (Rosa sect. Caninae). Heredity (Edinb) 2010; 104:113-20. [PMID: 19639009 DOI: 10.1038/hdy.2009.94] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The polyploid species in Rosa section Caninae (2n=21, 28 or 35) are characterized by an unusual reproductive system known as odd (or asymmetric) meiosis. Only two chromosome sets form bivalents in meiosis, whereas the remaining chromosomes are transmitted as univalents through the female germline. Evolution of ribosomal rRNA genes (rDNA) does not seem to be significantly affected by interlocus homogenization in dogroses. As a consequence, most species contain several rDNA families falling into two main clades (beta and gamma) thought to be differentially distributed between bivalent and univalent chromosomes, respectively. Here, we have investigated expression of rRNA gene families in five pentaploid species (R. canina, R. rubiginosa, R. dumalis, R. sherardii and R. caesia, 2n=35) and in one tetraploid (R. mollis, 2n=28). Using extensive sequencing of ITS clones and cleaved amplified polymorphism sequence (CAPS) analysis, we found that the beta-family was constitutively expressed in all species. However, there was large variation in the expression patterns of families constituting the gamma-clade. In addition, a single family can be active in one species, whereas silenced in another. The data show that the families on bivalent-forming chromosomes dominate rDNA expression in all dogrose species. We hypothesize that genes on bivalent genomes are stably expressed, whereas those on univalent genomes undergo variable levels of epigenetic silencing. Nonetheless, mosaic expression of univalent genomes could contribute to phenotypic variation between the species.
Collapse
Affiliation(s)
- L Khaitová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i. Laboratory of Molecular Epigenetics, Brno, Czech Republic
| | | | | | | |
Collapse
|
|
31
|
Roberts AV, Gladis T, Brumme H. DNA amounts of roses (Rosa L.) and their use in attributing ploidy levels. PLANT CELL REPORTS 2009; 28:61-71. [PMID: 18839177 DOI: 10.1007/s00299-008-0615-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Revised: 08/19/2008] [Accepted: 09/09/2008] [Indexed: 05/18/2023]
Abstract
The aims of the investigation were to characterise variability among the DNA amounts of roses and assess the predictability of ploidy levels from DNA amounts. Chromosome numbers in the genus Rosa range from 2n = 2x = 14 to 2n = 8 x = 56 and aneuploidy is rare. Published 2C DNA amounts range from 0.78 pg in R. xanthina Lindl. and R. sericea Lindl. (2n = 2x = 14) to 2.91 pg in R. canina L. (2n = 5x = 35). In this investigation, DNA amounts were estimated by flow cytometry of leaf nuclei stained with propidium iodide, using Petroselinum crispum (2C DNA amount = 4.46 pg) as the internal calibration standard. Ploidy levels based on DNA amounts (DNA ploidy) were assigned by comparing their DNA amounts with published DNA amounts and identifying peaks and intervening discontinuities in frequency distributions of DNA amounts. 2C DNA amounts ranged from 0.83 pg in R. ecae (2x = 2x = 14) to 3.99 pg in R. acicularis (2n = 8 x = 56). Differences in the 1Cx-values (2C DNA amount/ploidy values) were found among the taxonomic sections of Rosa. Ploidy levels could be confidently assigned to most species and cultivars, but the ploidy of some specimens in the section Caninae was uncertain for reasons attributed to genomic diversity and aneuploidy. Cytochimerism was detected in three cultivars of R. x alba. DNA ploidy was determined in 384 specimens representing 74 species and 5 horticultural classes.
Collapse
Affiliation(s)
- A V Roberts
- School of Health and Bioscience, University of East London, London, E15 4LZ, UK.
| | | | | |
Collapse
|
|
32
|
De Cock K, Vander Mijnsbrugge K, Breyne P, Van Bockstaele E, Van Slycken J. Morphological and AFLP-based differentiation within the taxonomical complex section Caninae (subgenus Rosa). ANNALS OF BOTANY 2008; 102:685-97. [PMID: 18723861 PMCID: PMC2712374 DOI: 10.1093/aob/mcn151] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS The taxonomical structure of the polymorphic subgenus Rosa section Caninae is highly complex due to the combination of some unusual features: the unique polyploid chromosomal constitution, the heterogamic canina meiosis, the ability to hybridize interspecifically, and the predominantly matroclinal inheritance. Although most taxonomists agree on the subdivision of the section into three morphologically well-defined groups (Rubigineae, Vestitae, and Caninae), they disagree on the existence of smaller groups such as Tomentellae. The aim was to gain insight in the taxonomical structure and investigate the interpopulation differentiation of the polymorphic section Caninae by analysing morphological and AFLP-based characters of the seven most common Belgian dog-rose taxa. METHODS The intersubsectional and -specific relationships within the dog-roses were examined using morphological and molecular-genetic markers. AFLP data were analysed with basic descriptive genetic statistics because of the lack of Hardy-Weinberg equilibrium due to the polyploid genetic structure and heterogamic meiosis. KEY RESULTS Both the morphological and AFLP-based analyses supported the subdivision of the dog-roses in three well-defined though partly overlapping groups, Rubigineae, Vestitae and Caninae. However, it was not possible to distinguish between the morphologically well-defined taxa within the same subsection using AFLP-based data. In addition, the results suggested a high similarity of Rosa balsamica with subsection Caninae taxa. Small-scale geographical AFLP-based differentiation was observed within several dog-rose taxa. Surprisingly, individuals sampled at one locality and belonging to morphologically distinct dog-rose taxa displayed higher genetic similarities in comparison to their congeners sampled at different localities. CONCLUSIONS The hybridogenic character of the dog-roses was reflected in the vague boundaries between the subsections and on the species level within the subsections. Indications were found for current or historical hybridization on the genetic structure of the population. No morphological or AFLP-based evidence was obtained to support the existence of the separate subsection Tomentellae.
Collapse
Affiliation(s)
- Katrien De Cock
- Research Institute for Nature and Forest (INBO), Scientific Institute of the Flemish Government, Kliniekstraat 25, B-1070 Brussels, Belgium
| | - Kristine Vander Mijnsbrugge
- Research Institute for Nature and Forest (INBO), Scientific Institute of the Flemish Government, Kliniekstraat 25, B-1070 Brussels, Belgium
| | - Peter Breyne
- Research Institute for Nature and Forest (INBO), Scientific Institute of the Flemish Government, Kliniekstraat 25, B-1070 Brussels, Belgium
- For correspondence. E-mail
| | - Erik Van Bockstaele
- Institute for Agricultural and Fisheries Research (ILVO), Scientific Institute of the Flemish Government, Burg. Van Gansbergelaan 96 bus 1,B-9820 Merelbeke, Belgium
| | - Jos Van Slycken
- Research Institute for Nature and Forest (INBO), Scientific Institute of the Flemish Government, Kliniekstraat 25, B-1070 Brussels, Belgium
| |
Collapse
|
|
33
|
Kovarik A, Werlemark G, Leitch AR, Souckova-Skalicka K, Lim YK, Khaitová L, Koukalova B, Nybom H. The asymmetric meiosis in pentaploid dogroses (Rosa sect. Caninae) is associated with a skewed distribution of rRNA gene families in the gametes. Heredity (Edinb) 2008; 101:359-67. [PMID: 18648391 DOI: 10.1038/hdy.2008.63] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In pentaploid dogroses, Rosa section Caninae (2n=5x=35), the pollen transmits one basic genome (x=7) derived from the seven segregating bivalents, whereas the egg transmits four basic genomes (4x=28) one set derived from the segregation of seven bivalents and three sets of univalent-forming chromosomes. Chromosomes from all five genomes carry 18-5.8-26S nuclear ribosomal DNA (rDNA) sites. This mode of sexual reproduction, known as permanent odd polyploidy, can potentially lead to the independent evolution of rDNA on bivalent- and univalent-forming chromosomes. To test this hypothesis, we analyzed rRNA gene families in pollen and somatic leaf tissue of R. canina, R. rubiginosa and R. dumalis. Six major rRNA gene families (alpha, beta, beta' gamma, delta and epsilon) were identified based on several highly polymorphic sites in the internal transcribed spacers (ITSs). At least two of the major rRNA gene families were found in each species indicating that rDNAs have not been homogenized across subgenomes. A comparison of ITS1 sequences from leaf and pollen showed differences: the shared beta rRNA gene family was more abundant among pollen clones compared to leaf clones and must constitute a major part of the rDNA loci on bivalent-forming chromosomes. The gamma and delta families were underrepresented in pollen genomes and are probably located predominantly (or solely) on the univalents. The results support the hypothesis that pentaploid dogroses inherited a bivalent-forming genome from a common proto-canina ancestor, a likely donor of the beta rDNA family. Allopolyploidy with distantly related species is likely to have driven evolution of Rosa section Caninae.
Collapse
Affiliation(s)
- A Kovarik
- Laboratory of Molecular Epigenetics, Academy of Sciences of the Czech Republic, v.v.i., Institute of Biophysics, Brno, Czech Republic.
| | | | | | | | | | | | | | | |
Collapse
|
|
34
|
Nybom H, Esselink GD, Werlemark G, Leus L, Vosman B. Unique genomic configuration revealed by microsatellite DNA in polyploid dogroses, Rosa sect. Caninae. J Evol Biol 2006; 19:635-48. [PMID: 16599938 DOI: 10.1111/j.1420-9101.2005.01010.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An allopolyploid complex with high genomic integrity has been studied. Dogroses transmit only seven chromosomes (from seven bivalents) through the pollen, whereas 21, 28 or 35 chromosomes (from seven bivalents and 14, 21 or 28 univalents) come from the egg cells. Seedlings derived from two interspecific crosses were analysed with flow cytometry and molecular markers to determine ploidy level, mode of reproduction and genomic constitution. Evidence was obtained for the formation of unreduced male and female gametes, which can take part in fertilization (producing seedlings with higher ploidy than the parental plants) or in apomictic reproduction. Random amplified polymorphic DNA (RAPD) and microsatellite analyses indicated that three seedlings (5%) were derived through apomixis, whereas the other 49 were hybrids. Bivalent formation appears to involve chromosomes that consistently share the same microsatellite alleles. Allele-sharing between the maternally transmitted and highly conserved univalent-forming chromosomes reflected the taxonomic distance between different genotypes. The frequently recombining bivalent-forming chromosomes were taxonomically less informative.
Collapse
Affiliation(s)
- H Nybom
- Balsgård-Department of Crop Science, Swedish University of Agricultural Sciences, Fjälkestadsvägen, Kristianstad, Sweden.
| | | | | | | | | |
Collapse
|